VISIR_OLD_SPC_PHOT(7)

📦
version 4.4.2 · 2 versions
, in debian bookworm, ubuntu noble

💖 VISIR_OLD_SPC_PHOT(7) 💖

okay bestie, welcome to visir_old_spc_phot — it's one of the visir recipes and honestly it's doing a lot, so grab a snack 🍓

✨ NAME ✨

visir_old_spc_phot — the Old DRS detector recipe for sensitivity computation in spectroscopy. yes she's an elder, no we don't disrespect her 💅

🌸 SYNOPSIS 🌸

esorex visir_old_spc_phot [OPTIONS] FILE.sof

🦋 DESCRIPTION 🦋

okay so this recipe is giving main character energy and it does three whole jobs:

  1. It estimates the dispersion relation using the atmospheric spectrum in a long-slit spectroscopy half-cycle frame.
  2. It also extracts the spectrum of an observed object using a combined frame.
  3. Lastly — and this is the one that named the recipe — it computes the spectral photometry of an observed standard star. ⭐

Now, the files in your Set Of Frames (the sof-file, iykyk) have to be tagged, and the tags are non-negotiable, bestie:

VISIR-Long-Slit-Spectroscopy-file.fits SPEC_CAL_PHOT
VISIR-Quantum-Efficiency-Calibration-file.fits SPEC_CAL_QEFF
VISIR-Atmospheric-Emission-Lines-Calibration-file.fits SPEC_CAL_LINES
VISIR-Spectroscopic-Standard-Star-Catalog.fits SPEC_STD_CATALOG

Plus — optional but iconic ✨ — you can add a bad pixel map with a PRO.CATG of SPEC_BPM to the Set Of Frames, tagged as:

  • BPM

👑 OPTIONS 👑

every single one of these has a full name for the EsoRex configuration file, and we're listing them all, because we do not skip details in this house 🫶
  • --nod <str> — an optional ASCII specification of the nodding positions, for when they're just… missing from the FITS-file 😭. The file has to be one line per input FITS-file, and each line is an integer (which gets ignored, rip) followed by a 0 or 1 to say object or sky. (str; default: ´NONE´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.nodding [default = NONE].
  • --auto_bpm <bool> — automatic detection and correction of bad pixels. (bool; default: True). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.auto_bpm [default = True].
  • --g <bool> — automatic filtering of glitches. (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.rem_glitch [default = False].
  • --p <bool> — automatic purging of half-cycle images whose median deviates more than a factor three from the mean of the medians of half-cycle images, or whose standard deviation deviates more than a factor three from the mean of their standard deviations. (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.purge_bad [default = False].
  • --union <bool> — combine images using their union, as opposed to their intersection. deprecated and ignored, see --combine_method — so like, it's here, it's just not doing anything 💀 (bool; default: True). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.union [default = True].
  • --rej <str> — each resulting pixel is the average of the corresponding (interpolated) pixel value in each jittered image. A positive value, n1, for the first of the two integers specifies that for each pixel the smallest n1 pixel values shall be ignored in the averaging. Similarly, a positive value, n2, for the second of the two integers specifies that for each pixel the largest n2 pixel values shall be ignored in the averaging. (str; default: ´0-0´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.rej [default = 0-0].
  • --plot <int> — the recipe can produce a number of predefined plots. Zero means that none of the plots are produced, while increasing values (e.g. 1 or 2) increases the number of plots produced. If the plotting fails a warning is produced, and the recipe continues — no drama, she moves on 💅. The default behaviour of the plotting is to use gnuplot (with option -persist). The recipe currently produces 1D-plots using gnuplot commands. The recipe user can control the actual plotting-command used by the recipe to create the plot by setting the environment variable CPL_PLOTTER. Currently, if CPL_PLOTTER is set it must contain the string ´gnuplot´. Setting it to ´cat > my_gnuplot_$$.txt´ causes a number of ASCII-files to be created, which each produce a plot when given as standard input to gnuplot (e.g. later or on a different computer). A finer control of the plotting options can be obtained by writing an executable script, e.g. my_gnuplot.pl, that executes gnuplot after setting the desired gnuplot options (e.g. set terminal pslatex color) and then setting CPL_PLOTTER to my_gnuplot.pl. The predefined plots include plotting of images. Images can be plotted not only with gnuplot, but also using the pnm format. This is controlled with the environment variable CPL_IMAGER. If CPL_IMAGER is set to a string that does not contain the word gnuplot, the recipe will generate the plot in pnm format. E.g. setting CPL_IMAGER to ´display - &´ will produce a gray-scale image using the image viewer display. (int; default: 0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.plot [default = 0].
  • --slit_skew <float> — distortion correction: skew of slit (degrees) (clockwise). (float; default: 0.52). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.phi [default = 0.52].
  • --spectrum_skew <float> — distortion correction: LMR skew of spectrum (degrees) (counter-clockwise). Not used in High Resolution. (float; default: 1.73). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.ksi [default = 1.73].
  • --vert_arc <float> — distortion correction: LR detector vertical curvature (pixel). Reduced by a factor 4 in MR. Not used in HR A-side. Increased by a factor 115/52 in HR B-side. (float; default: -0.8). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.eps [default = -0.8].
  • --hori_arc <float> — distortion correction: LMR detector horizontal curvature (pixel). Increased by a factor 1.5 in HR A-side. Reduced by a factor 2 in HR B-side. (float; default: 0.0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.delta [default = 0.0].
  • --off <str> — an optional ASCII specification of the offsets, in case those in FITS-headers are missing or just plain wrong 🙈. The file must consist of one line per input pair of FITS-files, and each line must consist of two numbers which represent the shift in pixels of that image relative to the first image. The first line should thus comprise two zeros. Correct FITS-header offsets mean that the i´th X offset can be gotten from Xoffset_0 - Xoffset_i, where Xoffset_i is the value of ESO SEQ CUMOFFSETX and likewise for Y. (str; default: ´NONE´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.offsets [default = NONE].
  • --ref <bool> — user-defined refining of the image offsets. See options objs and xcorr. (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.refine [default = False].
  • --objs <str> — the shift and add of images needs anchor points that typically are bright objects. These are normally detected automatically, but with user-defined refining of offsets enabled, they must be provided by the user through an ASCII file containing one line per anchor point, with each line consisting of its x and y coordinate (in pixels). This file is ignored with user-defined refining of offsets disabled. (str; default: ´NONE´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.objects [default = NONE].
  • --xcorr <str> — if user-defined refining of offsets is enabled, a cross-correlation of the images is performed. In order to speed up this process, this cross-correlation is performed only on smaller rectangles around the anchor points. The first two parameters is the half-size of this rectangle in pixels. The second pair is the maximum shift in x and y (pixels) evaluated by the cross-correlation on the rectangle. Used only if user-defined refining of offsets is enabled. (str; default: ´10-10-25-25´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.xcorr [default = 10-10-25-25].
  • --fixcombi <bool> — perform the distortion correction on the combined image, and not on each of the jittered images. This will reduce execution time and degrade the quality of the combined image — so it's the fast-and-slightly-worse option, choose wisely bestie 😭 (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.fixcombi [default = False].
  • --emis_tol <float> — the computation of the mean and standard deviation of the sensitivity is done for wavelengths with an atmospheric emissivity of at most emis_min + emis_tol * (emis_max - emis_min), where emis_min is the minimum emissivity in the observed wavelength range and emis_max is the ditto maximum. Thus emis_tol = 1 means that all wavelengths are included. (float; default: 1.0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.emis_tol [default = 1.0].
  • --destripe_iterations <int> — max number of destriping iterations (0 to disable destriping). Horizontal destriping is done first, and if no horizontal striping is detected, vertical destriping is performed. (int; default: 15). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.nstripe [default = 15].
  • --destripe_morpho <bool> — destripe with morphological cleaning. (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.mstripe [default = False].
  • --rl <int> — reject leftmost columns in spectrum extraction, zero means all columns on the left are used. In cross-dispersion mode a (small) negative number may be used (pixel). (int; default: 0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.reject_left [default = 0].

…and that's only part 1, bestie — hold on, there's more 💖

  • --rr <int> — reject the rightmost columns when you're doing spectrum extraction. Zero means all the columns on the right get used, no skipping. In cross-dispersion mode you can throw in a (small) negative number (pixel) (int; default: 0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.reject_right [default = 0].
  • --ro_noise <float> — the readout noise of the detector, bestie (float; default: 14.5). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.ron [default = 14.5].
  • --ox_sigma <float> — the sigma you wanna use for clipping in optimal extraction (float; default: 5.0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.optex_sigma [default = 5.0].
  • --ox_niters <int> — how many optimal extraction iterations to perform, like actually run it this many times (int; default: 2). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.optex_niters [default = 2].
  • --ox_smooth <int> — width of the smoothing window used along the spectral dimension during optimal extraction. Heads up, it's a median filter doing the work (int; default: 31). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.optex_smooth [default = 31].
  • --gain <float> — the detector gain, slay (float; default: 0.75). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.gain [default = 0.75].
  • --ox_kernel <int> — size of the square smoothing kernel, in pixels, applied to the science frame before optimal extraction (it's ignored during aperture extraction, so don't stress about it there). Also a median filter, periodt (int; default: 3). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot.optex_kernel [default = 3].
✨ lowkey important ✨ You can make a configuration file holding all these options, along with suitable default values. For the deets, go look at what the 'esorex --help' command tells you.

🌈 SEE ALSO 🌈

The full documentation for the visir pipeline can be downloaded as a PDF file using this URL right here:

ftp://ftp.eso.org/pub/dfs/pipelines/visir/visir-pipeline-manual-1.4.pdf

Wanna see an overview of all the existing ESO pipelines? It's on the web page https://www.eso.org/sci/software/pipelines/. 💅

Basic documentation about the EsoRex program itself lives at the esorex(1) man page.

You can also call the pipelines from python using the python-cpl package. Peep https://packages.python.org/python-cpl/index.html for more info. 🐍✨

The other recipes of the visir pipeline are visir_img_dark(7), visir_img_ff(7), visir_img_reduce(7), visir_img_trans(7), visir_old_img_combine(7), visir_old_img_phot(7), visir_old_spc_obs(7), visir_old_spc_obs_ech(7), visir_old_spc_phot_ech(7), visir_old_spc_wcal(7), visir_old_spc_wcal_ech(7), visir_old_util_destripe(7), visir_spc_reduce(7), visir_util_apply_calib(7), visir_util_clip(7), visir_util_convert_weight(7), visir_util_detect_shift(7), visir_util_img_std_cat(7), visir_util_join(7), visir_util_qc(7), visir_util_repack(7), visir_util_run_swarp(7), visir_util_spc_std_cat(7), visir_util_spc_txt2fits(7), visir_util_undistort(7).

💖 VERSION 💖

visir_old_spc_phot 4.4.2

👑 AUTHOR 👑

Lars Lundin <https://support.eso.org>

😭 BUG REPORTS 😭

Please report any problems to https://support.eso.org. Or, like, alternatively, you may send a report to the ESO User Support Department <usd-help@eso.org>.

📜 LICENSE 📜

This file is part of the VISIR Instrument Pipeline Copyright (C) 2004, 2005 European Southern Observatory.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA.

and that's a wrap bestie 🫶 this was visir_old_spc_phot, version 4.4.2, straight out of the VISIR_OLD_SPC_PHOT(7) man page — go forth and extract them spectra, mwah 💋✨

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